Contacts of the strand formed by residues 138 - 145 (chain A) in PDB entry 4WGK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ARG* 3.7 24.9 - - + -
109A ALA 3.2 14.6 - - - +
110A ASP* 3.9 18.8 - - + -
111A CYS* 3.5 5.8 - - - -
135A THR* 5.1 2.7 - - - -
136A ARG* 3.5 32.2 - - + +
137A LEU* 1.3 72.9 - - - +
139A SER* 1.3 59.8 + - - +
140A ARG* 4.0 22.6 + - - -
157A SER 4.0 1.7 - - - +
158A ILE* 3.8 1.0 - - - -
159A ASP* 2.7 46.1 + - - +
316A SER* 6.1 0.2 - - - -
324A TYR* 6.4 2.7 - + - -
327A GLU* 5.4 1.8 - - - -
336A PRO* 4.0 0.5 + - - +
337A GLY* 3.3 32.8 + - - -
713A ALA* 3.2 29.5 - - + +
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 3.3 2.4 - - - -
109A ALA 2.7 33.7 + - - -
111A CYS* 3.6 8.3 - - - -
138A TYR* 1.3 73.2 - - - +
140A ARG* 1.3 60.2 + - - +
156A VAL* 3.2 19.2 - - - +
157A SER 3.9 3.6 - - - -
158A ILE* 4.0 4.0 - - - +
226A GLY 3.8 7.9 - - - -
227A ILE* 3.3 30.1 - - - +
230A SER* 2.9 24.6 + - - -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLY 3.3 2.5 - - - -
108A ARG* 3.4 21.0 - - + +
138A TYR* 4.0 16.6 + - + +
139A SER* 1.3 78.6 + - - +
141A ALA* 1.3 61.4 + - - +
142A PHE* 3.8 5.3 - - + -
155A PHE 3.7 1.4 - - - +
156A VAL* 3.3 3.2 - - - -
157A SER 2.9 43.1 + - - +
159A ASP* 3.2 31.7 + - - -
316A SER* 5.7 0.4 + - - -
320A GLY* 4.9 4.4 + - - -
323A SER* 3.7 17.9 + - - -
324A TYR* 6.1 0.2 - - - +
327A GLU* 2.9 32.0 + - - -
342A VAL* 3.6 26.7 - - + -
343A ALA 3.3 23.0 + - - -
344A ALA* 3.7 20.7 - - + +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 3.4 5.5 - - - +
107A GLY 2.9 29.8 + - - +
140A ARG* 1.3 72.3 - - - +
142A PHE* 1.3 68.3 + - - +
143A ILE* 4.3 0.7 - - + -
154A VAL* 4.7 3.6 - - + -
155A PHE 3.5 4.3 - - - -
156A VAL* 3.9 8.7 - - + -
230A SER* 3.7 34.4 - - - +
231A ILE* 3.8 19.5 - - + +
234A ALA* 4.0 3.8 - - + +
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Residues in contact with PHE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY 3.5 3.4 - - - +
106A VAL* 3.5 21.8 - - + -
140A ARG 3.8 13.2 - - - -
141A ALA* 1.3 75.6 - - - +
143A ILE* 1.3 62.8 + - - +
144A MET* 3.7 16.6 - - + +
153A THR 3.5 1.4 - - - +
154A VAL* 3.4 3.5 - - - -
155A PHE* 2.8 49.6 + + + +
286A MET* 3.5 30.7 - - + -
296A LEU 3.4 20.9 - - - -
297A ILE* 3.6 23.3 - - + -
342A VAL* 3.9 24.7 - - + -
344A ALA* 3.5 27.1 - - + -
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A HIS 3.6 1.2 - - - +
104A ILE* 3.4 4.5 - - - -
105A GLY* 2.8 40.5 + - - +
141A ALA* 5.1 0.9 - - + -
142A PHE* 1.3 76.6 - - - +
144A MET* 1.3 70.3 + - - +
152A ARG* 4.6 4.5 - - + -
153A THR 3.3 8.7 - - - +
154A VAL* 4.0 12.3 - - + -
183A TYR* 3.6 41.5 - - + +
231A ILE* 3.7 32.5 - - + +
234A ALA* 3.8 10.1 - - + -
235A HIS* 3.7 11.2 - - - +
238A MET* 3.7 20.7 - - + +
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Residues in contact with MET 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR* 5.0 3.8 - - + -
103A HIS 3.4 5.8 - - - +
104A ILE* 4.7 7.4 - - + -
142A PHE* 3.7 25.8 - - + +
143A ILE* 1.3 84.4 - - - +
145A ALA* 1.3 62.6 + - - +
152A ARG* 3.2 5.5 - - - +
153A THR* 2.9 54.9 + - - +
154A VAL 5.5 0.2 - - - -
155A PHE* 4.9 8.1 - - + +
238A MET* 4.4 0.9 - - - -
243A ILE* 3.7 29.8 - - + -
284A LEU* 6.0 4.5 - - + -
286A MET* 4.7 12.3 - - - +
297A ILE* 5.9 2.9 - - + -
423A LEU* 3.7 12.5 - - + +
527A ILE* 6.1 0.2 - - + -
529A LEU* 4.0 22.4 - - + -
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR* 3.5 8.9 - - - +
103A HIS* 2.9 32.6 + - + +
144A MET* 1.3 77.5 - - - +
146A GLU* 1.3 67.5 + - - +
149A GLY* 4.1 10.1 - - - +
150A SER 4.0 4.5 - - - +
151A ASN 4.4 0.9 - - - -
152A ARG* 4.1 19.7 - - + +
238A MET* 3.8 20.0 - - + -
423A LEU* 3.6 9.6 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il